Loops were firstly called using the ABC Model. Since this method integrates ATAC-seq, H3K27ac and gene expression data when calling enhancer-promoter (E-P) pairs, we can be more confident we are truly calling loops. After defining E-P loops, differential loop calling was performed using a modified DESeq2 approach via Hictoolsr.
ABC model results
Activity (A) is calculated as the geometric mean of the read counts of ATAC-seq and H3K27ac chromatin immunoprecipitation sequencing (ChIP–seq) at element E, and Contact (C) as the KR-normalized Hi-C contact frequency between E and the promoter of gene G at 5-kb resolution
Download Enhancer_promoter_loops.csvDifferential loop analysis
Differential loop analysis was performed at 1000kb resolution (ie. regions were binned at 10kb windows).
Raw counts
Counts
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E-P pairs
DESeq2 res
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PCA
Top 500 most variable loops
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All loops
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MA plot
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